Chelsea have made a formal complaint to the football authorities about the referee Mark Clattenburg, whose handling of their 3-2 home defeat to Manchester United caused such controversy, alleging that he directed "inappropriate language" towards two of their players, with club officials briefing that one part of the allegation concerns language of a racist nature.

The west London club released a statement at eight o'clock, which brought a fresh twist to a tumultuous day. They did not reveal the identity of the players, although one of them is understood to have been the Nigeria international Mikel John Obi, a player that Sir Alex Ferguson, the United manager, felt had been lucky to avoid a red card from Clattenburg, in a game in which two Chelsea players, Branislav Ivanovic and Fernando Torres, did receive them.

Roberto Di Matteo, the Chelsea manager, was furious at Clattenburg's decisions, in particular the one to give Torres a second yellow card for diving while the assistant referee allowed Javier Hernández's winning goal to stand, despite him having come back from an offside position. Di Matteo went to see Clattenburg after the match, flanked by some of his backroom staff, and he was aware at the time of the grievances of his players. Mikel is understood to have visited Clattenburg in his room.

"We have a lodged a complaint to the Premier League match delegate with regards to inappropriate language used by the referee and directed at two of our players in two separate incidents during today's match," said a Chelsea spokesman. "The match delegate will pass the complaint to the Football Association. We will make no further comment at this time."

Clattenburg was not reachable for comment after Chelsea's allegations but a statement from Professional Game Match Officials said it "is aware of the allegations and they are being treated with the utmost seriousness. Mark will co-operate fully and welcomes the opportunity for the facts to be established. No further comment will be made until matter has been properly investigated."

It is understood that the other Chelsea player who felt he was the victim of offensive language from Clattenburg was white, with reports suggesting it was the Spaniard Juan Mata. Chelsea are fully aware of the severity of the allegation, particularly in the wake of the John Terry-Anton Ferdinand racist slur saga.

Terry did not play here, as he served the second part of his four-match domestic ban from the FA for the racist abuse of Ferdinand, the QPR defender, but Rio Ferdinand did play for United. He was the subject of cat-calls, his every touch booed and, after Hernández's winner, he struck a defiant celebratory pose that appeared to enrage the crowd, leading to missiles being thrown.

This was after Chelsea had chosen to support the Kick It Out anti-racism campaign and Terry mentioned his club's "pride" at backing the campaign in his programme notes. Terry wore an anti-racism badge for the day. All of the Chelsea players wore Kick It Out T-shirts in the warm-up; the United winger, Ashley Young, was the only player who did not. It was unclear whether he was making a statement. There were ironic cheers from the United supporters when the on-pitch announcer read out the anti-discrimination message and, over 90 frenetic minutes, there was also rancour between the benches, Ferguson clashing with Di Matteo and members of the Chelsea staff after Torres's red card and at full-time.

Rio Ferdinand shook hands beforehand with Ashley Cole, who had given evidence in support of Terry at the Chelsea captain's magistrates court trial for abusing Anton. It felt as though a line had attempted to be drawn under one of the modern game's most destructive episodes, only for another controversy to erupt.

Clattenburg was miked up throughout the game and he could be heard by his assistants and the fourth official. Their conversations would not have been recorded but they could, in theory, be in a position to assist any inquiry.

Di Matteo was furious at his post-match press conference, although he focused only on Clattenburg's decisions in relation to the match. "Yes, I have been in to see him," he said. "Surely, when he's going to watch the images he's going to realise that he made big mistakes.

"We are massively disappointed that these key decisions were wrong. It always seems to be in favour of the opposition. That's a massive disadvantage for us. I thought at 2-2, we looked like the team that were probably going to win the game. You don't want the referees to be a big influence in the game, you let the two teams play each other and play a good game, that's what everybody loves to watch."